GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Synechococcus elongatus PCC 7942

Best path

rocE, adiA, aguA, aguB, patA, patD, gabT, gabD

Also see fitness data for the top candidates

Rules

Overview: Arginine utilization in GapMind is based on MetaCyc pathways L-arginine degradation I via arginase (link); II via arginine succinyltransferase (link), III via arginine decarboxylase and agmatinase (link), IV via arginine decarboxylase and agmatine deiminase (link), V via arginine deiminase (link), VI (arginase 2, link), VII (arginase 3, link), VIII via arginase oxidase (link), IX via arginine:pyruvate transaminase (link), X via arginine monooxygenase (link), XIII via proline (link), and XIV via D-ornithine (link). Common intermediates are L-ornithine or L-proline. GapMind does not include pathways XI (link), which is poorly understood, or XII (link), which is not reported in prokaryotes.

71 steps (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rocE L-arginine permease
adiA arginine decarboxylase (AdiA/SpeA) Synpcc7942_1037 Synpcc7942_0707
aguA agmatine deiminase Synpcc7942_2402 Synpcc7942_2461
aguB N-carbamoylputrescine hydrolase Synpcc7942_2145
patA putrescine aminotransferase (PatA/SpuC) Synpcc7942_0943 Synpcc7942_0031
patD gamma-aminobutyraldehyde dehydrogenase Synpcc7942_0489
gabT gamma-aminobutyrate transaminase Synpcc7942_0943 Synpcc7942_0031
gabD succinate semialdehyde dehydrogenase Synpcc7942_1857 Synpcc7942_0489
Alternative steps:
AAP3 L-arginine transporter AAP3
arcA arginine deiminase
arcB ornithine carbamoyltransferase Synpcc7942_2514 Synpcc7942_0670
arcC carbamate kinase
arg-monooxygenase arginine 2-monooxygenase
aroD L-arginine oxidase Synpcc7942_0946
artJ L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) Synpcc7942_0248 Synpcc7942_0247
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA Synpcc7942_0249 Synpcc7942_1414
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) Synpcc7942_0248 Synpcc7942_0247
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH L-arginine:pyruvate transaminase Synpcc7942_2545 Synpcc7942_1794
aruI 2-ketoarginine decarboxylase Synpcc7942_0139
astA arginine N-succinyltransferase
astB N-succinylarginine dihydrolase
astC succinylornithine transaminase Synpcc7942_0943 Synpcc7942_0031
astD succinylglutamate semialdehyde dehydrogenase Synpcc7942_0489
astE succinylglutamate desuccinylase
atoB acetyl-CoA C-acetyltransferase
bgtB L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) Synpcc7942_2495
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Synpcc7942_2494
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Synpcc7942_2493 Synpcc7942_1893
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Synpcc7942_2492 Synpcc7942_0815
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1
davD glutarate semialdehyde dehydrogenase
davT 5-aminovalerate aminotransferase Synpcc7942_0943 Synpcc7942_0645
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Synpcc7942_0597
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Synpcc7942_0684
gbamidase guanidinobutyramidase Synpcc7942_2145
gbuA guanidinobutyrase
gcdG succinyl-CoA:glutarate CoA-transferase
gcdH glutaryl-CoA dehydrogenase
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB 4-guanidinobutyraldehyde dehydrogenase Synpcc7942_0489
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase
oraE D-ornithine 4,5-aminomutase, beta (E) subunit
oraS D-ornithine 4,5-aminomutase, alpha (S) subunit
ord 2,4-diaminopentanoate dehydrogenase
orr ornithine racemase
ortA 2-amino-4-oxopentanoate thiolase, alpha subunit
ortB 2-amino-4-oxopentanoate thiolase, beta subunit
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase
PRO3 pyrroline-5-carboxylate reductase Synpcc7942_2058
puo putrescine oxidase Synpcc7942_0369
put1 proline dehydrogenase
putA L-glutamate 5-semialdeyde dehydrogenase
puuA glutamate-putrescine ligase Synpcc7942_2296 Synpcc7942_2156
puuB gamma-glutamylputrescine oxidase
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Synpcc7942_0489
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA 1-pyrroline-5-carboxylate dehydrogenase
rocD ornithine aminotransferase Synpcc7942_0943 Synpcc7942_0645
rocF arginase
speB agmatinase

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory